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SHOW ONLY VARIANTS PRESENT AT HGMD

FREQUENCIES

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EXCLUDE ALL VARIANTS PRESENT IN 1000GENOMES 		DBSNP FREQUENCY

EXCLUDE ALL VARIANTS PRESENT IN DBSNP 		ESP6500 FREQUENCY

EXCLUDE ALL VARIANTS PRESENT IN EXOME SEQUENCING PROJECT

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EXCLUDE VARIANTS WITHOUT SIFT SCORE 		POLYPHEN2 SCORE

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CADD

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EXCLUDE VARIANTS WITHOUT M-CAP SCORE
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+ Genes 4

+ Genes associated with diseases 3

Genes at Omim

HLA-A, HLA-DRB1, RP1L1,
HLA-A {Hypersensitivity syndrome, carbamazepine-induced, susceptibility to}, 608579 (3)
HLA-DRB1 {Multiple sclerosis, susceptibility to, 1}, 126200 (3)
{Sarcoidosis, susceptibility to, 1}, 181000 (3)
RP1L1 Occult macular dystrophy, 613587 (3)

Genes at Clinical Genomics Database

HLA-A, RP1L1,
HLA-A Drug-induced toxicity, susceptibility to
RP1L1 Retinitis pigmentosa, autosomal recessive
Occult macular dystrophy

Genes at HGMD

Summary

Number of Variants: 80
Number of Genes: 4

Export to: CSV
  • Page 1 of 1

HLA-A
Omim - GeneCards - NCBI
Options Individual Chr
 RsId
 Pos
 Qual
 Ref
 Alt
 Filter Gen
 Read Depth Effect Impact Func Class 1kgenomes dbSNP ESP6500 Sift PP2 CADD M-CAP CLINVAR HI Score
View combined sample_68.variant29 6 rs9256983
dbSNP Clinvar 		29911228 9074.82 A C,T,G PASS 1/3 344 NON_SYNONYMOUS_CODING MODERATE None 0.05571 0.18950 0.65 0.00 None None None None None None HLA-A|0.043055872|64.8%

HLA-DRB1
Omim - GeneCards - NCBI
Options Individual Chr
 RsId
 Pos
 Qual
 Ref
 Alt
 Filter Gen
 Read Depth Effect Impact Func Class 1kgenomes dbSNP ESP6500 Sift PP2 CADD M-CAP CLINVAR HI Score
View combined sample_68.variant29 6 rs769779152,rs17878703
dbSNP Clinvar 		32552137 4170.99 G GA... PASS 1/3 63 FRAME_SHIFT HIGH None None None None None None None HLA-DRB1|0.032266025|68.49%

HLA-DRB5
Omim - GeneCards - NCBI
Options Individual Chr
 RsId
 Pos
 Qual
 Ref
 Alt
 Filter Gen
 Read Depth Effect Impact Func Class 1kgenomes dbSNP ESP6500 Sift PP2 CADD M-CAP CLINVAR HI Score
View combined sample_68.variant29 6 rs1071748
dbSNP Clinvar 		32489933 349.68 T C,G,A PASS 1/3 44 NON_SYNONYMOUS_CODING MODERATE None 0.39 0.00 None None None None None None HLA-DRB5|0.020830666|73.74%

RP1L1
Omim - GeneCards - NCBI
Options Individual Chr
 RsId
 Pos
 Qual
 Ref
 Alt
 Filter Gen
 Read Depth Effect Impact Func Class 1kgenomes dbSNP ESP6500 Sift PP2 CADD M-CAP CLINVAR HI Score
View combined sample_68.variant29 8 rs9657518
dbSNP Clinvar 		10467589 7507.51 T C,... PASS 1/3 253 NON_SYNONYMOUS_CODING MODERATE None 0.44149 0.44150 None None None None None None RP1L1|0.000840698|96.44%
Omim - GeneCards - NCBI
Options Individual Chr
 RsId
 Pos
 Qual
 Ref
 Alt
 Filter Gen
 Read Depth Effect Impact Func Class 1kgenomes dbSNP ESP6500 Sift PP2 CADD M-CAP CLINVAR HI Score
View combined sample_68.variant29 1 rs766640917,rs869193536
dbSNP Clinvar 		207959122 763.59 CTTTT C,... PASS 1/3 30 None None None None None None None None None CD46|0.000253388|99.61%
View combined sample_68.variant29 1 rs879176665
dbSNP Clinvar 		211665390 215.66 GG... G,... PASS 1/3 13 None None None None None None None None None RD3|0.062363918|59.23%
View combined sample_68.variant29 2 rs750488613
dbSNP Clinvar 		55516911 5542.8 AA... AA... PASS 1/3 113 None None None None None None None None None CCDC88A|0.425281284|19.33%
View combined sample_68.variant29 3 rs535322489
dbSNP Clinvar 		58351660 308.66 CT CT... PASS 1/3 36 None None None 0.09385 0.09385 None None None None None None PXK|0.375653665|22.34%
View combined sample_68.variant29 3 rs201120646,rs763342139
dbSNP Clinvar 		116746457 2050.69 GTTA GT... PASS 1/3 29 None None None 0.00240 0.35840 None None None None None None LSAMP|0.999921905|0.17%
View combined sample_68.variant29 3 . 168542454 302.92 TCA TC... PASS 1/3 26 None None None None None None None None None None
View combined sample_68.variant29 4 rs754007285
dbSNP Clinvar 		110569880 528.08 CAAAA CA... PASS 1/3 26 None None None None None None None None None CCDC109B|0.014014782|77.87%
View combined sample_68.variant29 5 rs3086385,rs61641313
dbSNP Clinvar 		36166827 513.97 CT CT... PASS 1/3 36 None None None None None None None None None SKP2|0.862819051|4.42%
View combined sample_68.variant29 5 rs368393930
dbSNP Clinvar 		150506104 278.02 AA... AA... PASS 1/3 12 None None None 0.11182 0.11180 None None None None None None ANXA6|0.284174792|28.78%
View combined sample_68.variant29 6 rs34735056
dbSNP Clinvar 		47547070 425.71 T TA... PASS 1/3 24 None None None 0.17870 None None None None None None CD2AP|0.343657419|24.58%
View combined sample_68.variant29 8 rs796300144,rs879072194
dbSNP Clinvar 		11279882 1681.86 GGT TG... PASS 1/3 72 None None None None None None None None None FAM167A-AS1|0.000825171|96.52%,FAM167A|0.032787665|68.25%
View combined sample_68.variant29 8 . 22990193 931.15 TT... TT... PASS 1/3 51 None None None None None None None None None None
View combined sample_68.variant29 9 rs769675551
dbSNP Clinvar 		139875318 798.43 CCATT CC... PASS 1/3 30 None None None None None None None None None PTGDS|0.006824526|83.66%
View combined sample_68.variant29 9 rs559874845,rs386416466
dbSNP Clinvar 		139965120 559.16 A AT... PASS 1/3 46 None None None 0.63918 0.63920 None None None None None None None
View combined sample_68.variant29 10 rs150421371
dbSNP Clinvar 		91007603 263.07 TT... TT... PASS 1/3 6 None None None None None None None None None LIPA|0.012788499|78.66%
View combined sample_68.variant29 11 . 31833848 173.95 C CT... PASS 1/3 33 None None None None None None None None None PAX6|0.995427329|0.78%
View combined sample_68.variant29 12 rs149288740,rs56857131
dbSNP Clinvar 		56415078 1436.61 T TC... PASS 1/3 43 None None None 0.37320 0.37320 None None None None None None IKZF4|0.415996518|19.79%
View combined sample_68.variant29 12 rs11171845,rs142212258,rs386376624
dbSNP Clinvar 		56826758 1965.02 A G,... PASS 1/3 31 None None None 0.39537 0.39540 None None None None None None TIMELESS|0.36130758|23.36%
View combined sample_68.variant29 12 rs63397860,rs60146346
dbSNP Clinvar 		79843703 2626.04 CGTGT CG... PASS 1/3 77 None None None None None None None None None SYT1|0.883250678|3.9%
View combined sample_68.variant29 12 rs57265159
dbSNP Clinvar 		113623326 3616.78 G GT... PASS 1/3 60 None None None None None None None None None None
View combined sample_68.variant29 14 rs878909286
dbSNP Clinvar 		90871914 543.96 CT CT... PASS 1/3 60 None None None None None None None None None CALM1|0.999937868|0.15%
View combined sample_68.variant29 14 rs796251496,rs565756487,rs10603293
dbSNP Clinvar 		92588155 5882.55 ATTTT A,... PASS 1/3 125 None None None 0.53330 None None None None None None NDUFB1|0.068300052|57.87%
View combined sample_68.variant29 16 rs796127928
dbSNP Clinvar 		11797365 946.38 TA... TA... PASS 1/3 42 None None None None None None None None None TXNDC11|0.086563935|53.85%
View combined sample_68.variant29 17 . 40359505 488.51 GC... GC... PASS 1/3 34 None None None None None None None None None STAT5B|0.791650824|6.07%
View combined sample_68.variant29 17 rs8075486,rs56406015
dbSNP Clinvar 		73208205 1082.95 G T,... PASS 1/3 20 None None None 0.02316 0.02316 None None None None None None NUP85|0.371302082|22.64%
View combined sample_68.variant29 17 rs147486363
dbSNP Clinvar 		79093029 818.05 TG... T,... PASS 1/3 21 None None None 0.33287 0.33290 None None None None None None AATK|0.00450864|86.39%
View combined sample_68.variant29 18 . 9959718 1062.46 CA... CA... PASS 1/3 108 None None None None None None None None None VAPA|0.409485069|20.21%
View combined sample_68.variant29 19 rs4804096,rs572607972
dbSNP Clinvar 		9203785 3301.25 C T,... PASS 1/3 59 None None None None None None None None None None
View combined sample_68.variant29 1 . 1395449 36.35 ATTT AT... PASS 1/3 20 None None None None None None None None None ATAD3C|0.007544174|83.02%
View combined sample_68.variant29 19 rs796088008,rs560286873
dbSNP Clinvar 		47524151 1237.46 GCCC GC... PASS 1/3 29 None None None None None None None None None NPAS1|0.050860776|62.41%
View combined sample_68.variant29 3 . 29322605 90.8 GT GT... PASS 1/3 16 None None None None None None None None None RBMS3|0.934703314|2.66%
View combined sample_68.variant29 3 . 179342360 940.2 TA... TA... PASS 1/3 39 None None None None None None None None None NDUFB5|0.177986776|39.3%
View combined sample_68.variant29 4 rs776142668
dbSNP Clinvar 		57861096 251.93 GA... GA... PASS 1/3 10 None None None None None None None None None POLR2B|0.866806985|4.32%
View combined sample_68.variant29 4 rs796375311,rs749565123,rs58884223
dbSNP Clinvar 		62775479 241.45 ATG A,... PASS 1/3 17 None None None None None None None None None ADGRL3|0.887869356|3.75%
View combined sample_68.variant29 6 rs281860816,rs9274531,rs141479977,rs386406641,rs202167390
dbSNP Clinvar 		32634564 423.69 A T,... PASS 1/3 19 None None None 0.30511 0.30510 None None None None None None HLA-DQB1|0.132406558|45.55%
View combined sample_68.variant29 6 rs762964151
dbSNP Clinvar 		123869769 1374.18 TAAA TA... PASS 1/3 34 None None None None None None None None None TRDN|0.11061284|49.08%
View combined sample_68.variant29 7 . 70249728 660.01 TA... TA... PASS 1/3 13 None None None None None None None None None AUTS2|0.998368801|0.51%
View combined sample_68.variant29 7 rs878902292
dbSNP Clinvar 		142139624 355.03 GCA GC... PASS 1/3 34 None None None None None None None None None None
View combined sample_68.variant29 8 rs72423486,rs35791396
dbSNP Clinvar 		63502434 64.41 TT... T,... PASS 1/3 11 None None None None None None None None None NKAIN3|0.347255626|24.34%
View combined sample_68.variant29 10 . 24498289 434.96 GAA GA... PASS 1/3 60 None None None None None None None None None KIAA1217|0.163143499|41.11%
View combined sample_68.variant29 11 rs752759263
dbSNP Clinvar 		93454831 1373.33 GG... GG... PASS 1/3 26 None None None None None None None None None CEP295|0.00978904|81%
View combined sample_68.variant29 14 rs770604295
dbSNP Clinvar 		59836862 581.69 CT... CT... PASS 1/3 76 None None None None None None None None None DAAM1|0.619833146|11.09%
View combined sample_68.variant29 14 rs113558496,rs3075829
dbSNP Clinvar 		77901758 736.13 G GA... PASS 1/3 43 None None None None None None None None None VIPAS39|0.234961571|32.92%
View combined sample_68.variant29 14 rs72042212,rs60394937
dbSNP Clinvar 		104491086 446.86 TA... T,... PASS 1/3 14 None None None None None None None None None TDRD9|0.024054474|72.2%
View combined sample_68.variant29 15 rs748321013
dbSNP Clinvar 		45445692 810.83 AT... AT... PASS 1/3 49 None None None None None None None None None DUOX1|0.119511675|47.53%
View combined sample_68.variant29 15 rs369451587,rs71432251
dbSNP Clinvar 		48064554 862.23 C CG... PASS 1/3 54 None None None None None None None None None SEMA6D|0.872174744|4.17%
View combined sample_68.variant29 16 . 50706407 117.58 CGTGT CG... PASS 1/3 15 None None None None None None None None None SNX20|0.008454496|82.2%
View combined sample_68.variant29 15 rs796286767
dbSNP Clinvar 		98513086 61.72 CTT CT... PASS 1/3 24 None None None None None None None None None ARRDC4|0.053899861|61.5%
View combined sample_68.variant29 16 . 21732553 660.33 TA... TA... PASS 1/3 36 None None None None None None None None None OTOA|0.045412102|64.09%
View combined sample_68.variant29 16 rs72416804
dbSNP Clinvar 		68014739 185.15 T TA... PASS 1/3 11 None None None 0.36262 0.36260 None None None None None None None
View combined sample_68.variant29 19 . 42497653 234.94 GC... GC... PASS 1/3 21 None None None None None None None None None ATP1A3|0.149065263|43.12%
View combined sample_68.variant29 1 rs200568394
dbSNP Clinvar 		162338228 508.03 CA... C,... PASS 1/3 33 None None None 0.86322 0.86320 None None None None None None NOS1AP|0.368787002|22.78%,C1orf226|0.034731923|67.54%
View combined sample_68.variant29 19 rs371907605
dbSNP Clinvar 		49685708 3050.35 CC... CC... PASS 1/3 65 None None None None None None None None None TRPM4|0.032654157|68.31%
View combined sample_68.variant29 2 rs10804413
dbSNP Clinvar 		241706166 907.74 T A,... PASS 1/3 16 None None None None None None None None None KIF1A|0.102859335|50.62%
View combined sample_68.variant29 2 . 42996709 392.62 AT... A,... PASS 1/3 13 None None None None None None None None None HAAO|0.143962065|43.87%
View combined sample_68.variant29 2 rs79198208,rs10194887,rs59832078,rs59476187
dbSNP Clinvar 		86368042 511.6 A C,... PASS 1/3 5 None None None None None None None None None PTCD3|0.046279817|63.82%
View combined sample_68.variant29 2 rs796781337,rs549405138,rs796498353,rs397987770
dbSNP Clinvar 		216274853 797.88 AAC A,... PASS 1/3 26 None None None 0.39400 None None None None None None FN1|0.99982615|0.22%
View combined sample_68.variant29 3 rs751568064
dbSNP Clinvar 		47143087 203.78 AG... AG... PASS 1/3 28 None None None None None None None None None SETD2|0.695117381|8.64%
View combined sample_68.variant29 3 rs34045680,rs397784250,rs56195200
dbSNP Clinvar 		129693108 954.24 T TC... PASS 1/3 17 None None None 0.95827 0.95830 None None None None None None None
View combined sample_68.variant29 3 rs113722473
dbSNP Clinvar 		195473756 1818.96 CG... C,... PASS 1/3 101 None None None None None None None None None MUC4|0.005441696|85.29%
View combined sample_68.variant29 6 . 56971106 154.31 CTT CT... PASS 1/3 49 None None None None None None None None None ZNF451|0.195609074|37.21%
View combined sample_68.variant29 7 rs35141756,rs796615750
dbSNP Clinvar 		123671547 2973.66 CA C,... PASS 1/3 216 None None None 0.17272 0.18410 None None None None None None TMEM229A|0.025034265|71.78%
View combined sample_68.variant29 8 rs5891075
dbSNP Clinvar 		39871298 2410.06 T TT... PASS 1/3 40 None None None 0.01977 0.21850 None None None None None None IDO2|0.034637935|67.56%
View combined sample_68.variant29 9 . 115635917 3306.71 CTT C,... PASS 1/3 146 None None None 0.32129 None None None None None None SNX30|0.232108411|33.19%
View combined sample_68.variant29 11 rs140876943,rs61903690
dbSNP Clinvar 		89909096 553.68 A G,... PASS 1/3 35 None None None 0.04153 0.06250 None None None None None None NAALAD2|0.080206845|55.11%
View combined sample_68.variant29 12 . 98938907 86.28 GT G,... PASS 1/3 54 None None None None None None None None None TMPO|0.660221751|9.68%
View combined sample_68.variant29 12 . 118502242 146.81 GT GT... PASS 1/3 222 None None None None None None None None None VSIG10|0.023302825|72.52%
View combined sample_68.variant29 13 . 100617424 111.16 GA GA... PASS 1/3 37 None None None None None None None None None ZIC5|0.189825813|37.83%
View combined sample_68.variant29 14 rs869149581
dbSNP Clinvar 		76662780 90.62 GTT GT... PASS 1/3 32 None None None None None None None None None GPATCH2L|0.283468162|28.84%
View combined sample_68.variant29 16 rs769576082,rs9302778
dbSNP Clinvar 		88723538 758.73 TGG TG... PASS 1/3 31 None None None None None None None None None MVD|0.030828097|69.02%
View combined sample_68.variant29 18 rs745349765,rs71160827
dbSNP Clinvar 		60025458 1857.79 GTT G,... PASS 1/3 91 None None None None None None None None None TNFRSF11A|0.301687463|27.52%
View combined sample_68.variant29 19 . 2993918 216.13 CAAAA CA... PASS 1/3 39 None None None None None None None None None TLE6|0.001439035|93.1%
View combined sample_68.variant29 20 rs761292734
dbSNP Clinvar 		13561632 238.55 TA TA... PASS 1/3 15 None None None None None None None None None TASP1|0.738899515|7.4%
View combined sample_68.variant29 20 rs556071197
dbSNP Clinvar 		60709530 882.74 CTT CT... PASS 1/3 54 None None None None None None None None None LSM14B|0.085668924|54.01%
View combined sample_68.variant29 1 rs60036848
dbSNP Clinvar 		219366400 250.22 T TG... PASS 1/3 38 None None None 0.00220 0.73340 None None None None None None LYPLAL1|0.093393579|52.51%
View combined sample_68.variant29 21 rs143256471
dbSNP Clinvar 		46915985 1130.96 CA... CA... PASS 1/3 23 None None None None None None None None None COL18A1|0.045578537|64.02%,SLC19A1|0.006805855|83.69%
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